Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.     

甲胎蛋白分子演化的生物信息学分析

甲胎蛋白（AFP）是类白蛋白家族成员蛋白之一,在生物个体发育以及肝癌发生发展中起重要作用. 为了研究AFP的系统发生,并以此探讨系统发育与个体发育的关系,运用生物信息学手段,分析了不同物种中类白蛋白家族成员的进化关系,并对各分子的白蛋白结构域进行了进化归类.同时,对不同物种的白蛋白（ALB）和AFP之间包含启动子、抑制子和增强子在内的约14?kb的核苷酸序列进行了比较分析. 研究从系统发育的角度阐释了AFP分子及其基因调控机制的演化方式,为更好的认识AFP在机体生理和病理状态的作用建立了理论分析的基础.     

Rapid genome evolution in Pms 1 region of rice revealed by comparative sequence analysis

Pms1, a locus for photoperiod sensitive genic male sterility in rice, was identified and mapped to chromosome 7 in previous studies. Here we report an effort to identify the candidate genes for Pms1 by comparative sequencing of BAC clones from two cultivars Minghui 63 and Nongken 58, the parents for the initial mapping population. Annotation and comparison of the sequences of the two clones resulted in a total of five potential candidates which should be functionally tested. We also conducted com-parative analysis of sequences of these two cultivars with two other cultivars, Nipponbare and 93-11, for which sequence data were available in public databases. The analysis revealed large differences in sequence composition among the four genotypes in the Pms1 region primarily due to retroelement activity leading to rapid recent growth and divergence of the genomes. High levels of polymorphism in the forms of indels and SNPs were found both in intra- and inter-subspecific comparisons. Dating analysis using LTRs of the retroelements in this region showed that the substitution rate of LTRs was much higher than reported in the literature. The results provided strong evidence for rapid genomic evolution of this region as a consequence of natural and artificial selection.     

Component-based software reliability analysis incorporating imperfect debugging and change-point

Against the deficiencies of component-based software （CBS） reliability modeling and analysis,for instance,importing too many assumptions,paying less attention to debugging process without considering imperfect debugging and change-point （CP） problems adequately,an approach of CBS reliability process analysis is proposed which incorporates the imperfect debugging and CP.First,perfect/imperfect debugging and CP are reviewed.Based on the queuing theory,a multi-queue multichannel and infinite server queuing model （MMISQM） is presented to sketch the integration test process of CBS.Meanwhile,considering the effects of imperfect debugging and CP,expressions for fault detection and correction are derived based on MMISQM.Numerical results demonstrate that the proposed model can sketch the integration test process of CBS with preferable performance which outperforms other models.     

A comparative analysis on two solar proton events

This paper presents a comparative analysis on the two Solar Proton Events (SPE), which occurred on 14 July 2000 (Bastille Day) and 28 October 2003 (28OCT03) respectively. It is found that although the peak flux of the latter seemed to be greater than that of the former based on geostationary observations, the maximum intensities of the energetic protons (>10 MeV and 30 MeV) during the Bastille Day event were all higher than those of the 28OCT03 event according to the interplanetary observations. Further analysis indicated that the quantity of the seed particles, which could be accelerated to the energies exceeding 10 and 30 MeV by the Coronal Mass Ejection (CME)-driven shock on 14 July 2000, was far larger than that of the 28OCT03 event. In the Bastille Day case, when the CME approached to the height around 14 R⊙, the CME-driven shock would reach its maximum capacity in accelerating the solar en- ergetic protons (>100 MeV). In contrast, on 28 October 2003, when CME approached to the height about 58R⊙, the CME-driven shock reached its highest potential in accelerating the solar energetic protons of the same category. At this moment, the peak flux (>100 MeV) was about 155 pfu, which was much lower than 355 pfu measured on 14 July 2000. This demonstrated that in the Bastille Day event, the quantity of the seed particles, which could be accelerated to the energy beyond 100 MeV, was significantly larger than its counterpart in the 28OCT03 case. Therefore, the peak flux of an SPE event depends not only on the interplanetary intensity of the solar energetic particles, but also on the velocity of the associated CME-driven shock, and the quantity of the seed particles as well as on the interplanetary magnetic en- vironment. This paper also reveals that the magnetic sheath associated with ICME on 28 October 2003 captured a large number of solar energetic protons, including those having energy greater than 100 MeV.     

非理想信道信息对于多用户MIMO系统的性能影响分析

摘要：针对闭环系统中存在反馈时延及接收端存在信道估计误差的情况,分析了非理想信道信息对基于天线选择方案的闭环多用户MIMO系统的性能影响。文中推导了中断容量及误比特率的解析表达式,通过理论分析表明反馈时延及估计误差会使得整个系统的性能下降,同时分析了多用户分集对系统的影响。最后通过数值仿真验证了理论分析的正确性。     

面向动态演化的复杂网构软件系统可靠性分析方法

 网构软件是Internet上各种软件实体以各种协同方式实现跨网络的互连、互通和协作的软件系统，动态演化是其基本特征，演化过程中会导致软件系统失效，面向动态演化的网构软件可靠性分析成为新的技术难题。首先分析构件接口交互之间的协议关系和网构软件动态演化错误传播可达性，提出通过错误传播可达图来界定构件动态演化错误的影响范围，并建立错误传播可达图生成过程模型；其次，为有效解决Markov状态空间“爆炸”的问题，利用错误传播可达图来生成Markov状态转移图，提出基于Markov的网构软件动态演化可靠性分析方法；最后通过案例分析来验证该方法的有效性。     

A novel comparative molecule/pseudo receptor interaction analysis

Quantitative structure-activity relationship (QSAR) becomes an important tool in the modern basic chemis- try. In the 1960s, Hansch et al.[1] proposed Hansch- Fujita method to express the relationships between ac- tivities and parameters. Free et al.[2] d…     

简·爱与苔丝的性格及其命运对比分析

《简·爱》与《德伯家的苔丝》都是英国女性主义文学的经典之作。小说的主人公简·爱和苔丝作为女性勇敢反抗桎梏、追求自身幸福的典型形象,得到了广泛的讨论和认同。但两者的不同命运结局却让人唏嘘不已。通过对比分析简·爱和苔丝在面对人生遭遇和爱情时所表现出来的性格差异,可以探讨女性的性格与命运的关系。     

西部主要城市进化过程中创新力比较研究

根据城市创新理论,选取西安、重庆、成都、乌鲁木齐、兰州、南宁6个西部大城市,结合国内外的城市创新综合能力评价指标体系,着重分析了西部城市进化过程中的创新特点,提出了城市进化过程中所面对的问题,并给出应对对策及建议。     

3个茶树品种WOX基因家族的进化及密码子偏好性比较

【目的】WOX基因家族在模式植物组织培养中扮演着重要的分子调控角色。非模式植物WOX基因家族的系统发育和密码子使用偏好性研究有助于探索遗传进化规律和基因表达特征,进而为其转基因体系构建提供指导。【方法】利用生物信息学方法在3个茶树品种全基因组数据中鉴定WOX基因;通过ClustalX 2.1和MEGA X软件探索它们的进化规律。运用Perl语言、Codon W 1.4.2程序和SPSS 23.0等软件分析3个茶树品种WOX基因编码序列,探究它们的密码子使用偏好模式;基于ENc-GC_3s、PR2分析和中性分析结果解析影响密码子偏好的主要因素。【结果】共鉴定出42个WOX成员,其中‘云抗10号’(CSA)11个,‘舒茶早’(CSS)18个,‘云南野生古茶DASZ’(DASZ)13个,系统发育揭示3个茶树品种WOX基因在进化上存在较强的保守性。密码子偏好性分析揭示,3个茶树品种WOX基因密码子都偏好使用A/T和以A/T结尾;CSA和DASZ的WOX基因密码子使用模式相似,表明两者亲缘关系较近;以CSA和CSS作为转基因受体时,3个茶树品种WOX基因中个别密码子需优化;烟草是3个茶树品种WOX基因的最佳异源表达受体;ENc-GC_3s绘图、PR2分析和中性分析表明自然选择是影响3个茶树品种WOX基因密码子使用偏倚的主要因素。【结论】3个茶树品种WOX基因进化上较保守,密码子偏好使用A/T和以A/T结尾,且密码子偏好原因主要是自然选择;揭示出转茶树时密码子的优化信息和烟草为最佳异源表达受体的结果。     

5种鼠类针毛结构的扫描电镜分析

通过光镜和扫描电镜对社鼠、白腹巨鼠、黑线姬鼠、青毛鼠和黄胸鼠背部针毛的形态结构进行了对比研究,其针毛上的鳞片类型可分为波状、指状、多鳞状、杂波状和锯齿杯状5种.单因素方差分析和多重比较表明,各鳞片类型在不同鼠种中的比例差异显著,具有种的特异性,可以作为鼠类分类的参考指标.     

A comparative analysis of tissue gene expression data from high-throughput studies

High-throughput technologies were employed over the past decade to study the expression profiles of cells and tissues.There are large collections of accumulated data from public databases and numerous research articles were published on these data.In the current study,we performed meta-analysis on the gene expression data from human liver and kidney tissues produced from five different technologies:EST,SAGE,MPSS,microarray,and RNA-Seq.We found RNA-Seq was the most sensitive in the number of genes it detected while SAGE and MPSS were the least sensitive.For the genes detected by all the platforms,there were generally good correlations to the measured expression levels of corresponding genes.We further compared detected genes to liver/kidney proteomics data from the Human Protein Atlas,and found 960 of the 8764 genes only detected by RNA-Seq were validated by proteomics results.In conclusion,RNA-Seq is a more sensitive and consistent technology compared to the other four high-throughput platforms,though their results are in general agreement.Average coverage was determined to be the preferred measurement to represent gene expression levels by RNA-Seq data and will be used in future works.     

分离式和交际法听力测试的比较

听力测试是语言测试的重要组成部分，也是了解个体语言行为的一种重要手段。数十年来，分离式听力测试模式被广泛应用于各类英语考试中。然而，近年来有很多学者对分离式测试的有效性提出了质疑，他们认为现行的英语听力理解考试不能真正体现受测者的实际语言运用能力。同时，交际法听力测试随着交际法理论的发展而越来越受到人们的关注。这两种测试各有利弊，不能只是简单舍弃，而应扬长避短。     

Game theoretic simulation on the mimicry honeypot

A mimicry honeypot framework based on game theory is presented in our work, which can calculate the equilibrium strategy of the deceptive game using non-cooperative incomplete dynamic game theory, and make decisions for the mimicry framework to deploy the simple service, the honeypot and the fake honeypot. A mimicry prototype is implemented using NS2 platform, and simulation experiments are launched to validate the decision-making result and the deceptive performance of the mimicry honeypot. The empirical study shows that the mimicry honeypot framework based on game theory can be able to influence the equilibrium strategy results by dynamically changing the deployment vector of the mimicry system. It validates that the mimicry honeypot framework has better flexibility, activeness and fraudulence than the traditional honeypot.     

技术进化的数量分析

技术进化是技术哲学中的一个重要课题。技术进化实质上就是对其进行描述的标度数量的增长并发生质的提高过程。首先阐述了技术是一种复杂的社会现象，分析了技术进化的历程，给出了技术进化的标度，从量的视角探讨了技术进化的动力模型，同时对技术进化过程中的突变进行了定量分析。为技术进化的数量研究，提供了一条有益的途经。     

细叶楠木材的挥发性成分对比分析

【目的】通过对细叶楠与其同属树种及相近树种的木材挥发性化学成分的对比分析,归纳总结出这些木材之间的区别。【方法】通过固相微萃取取样方法和GC-MS分析技术对木材挥发性成分进行分析。【结果】不同地区细叶楠木材挥发性成分的总离子流图相似度高,对应峰的保留时间基本一致,相关系数高,显著性较大。细叶楠木材的挥发性成分主要为多种萜类化合物,且均含有3,7-愈创木二烯、α-紫穗槐烯、δ-荜澄茄烯、十四醛、榄香醇、愈创蓝油烃和7-乙酰基-2-羟基-2-甲基-5-异丙基二环[4,3,0]壬烷等7种特征化合物。细叶楠与其同属树种、相近树种的木材挥发性成分有较大差异,可以此作为区分细叶楠木材与其他树种木材的参考依据。【结论】细叶楠木材挥发性成分的GC-MS分析可用来作为识别木种的一种新方法,但要求必须包含7种特征化合物,且保留时间基本相同,相关系数必须大于0.750。     

小高层结构屋顶不同的TMD设置方式减震对比分析

根据屋顶水箱和保温层对房屋整体结构减震的作用,建立采用铅芯橡胶支座的3种不同屋顶的TMD控制装置的小高层结构模型,即单水箱屋顶TMD、双水箱屋顶TMD和屋顶保温层TMD.在此基础上运用有限元分析和动力时程分析方法对控制装置的减震效果进行计算对比.对比结果表明,3种屋顶TMD控制装置均有明显的减震效果;当质量比控制在3%以内时,质量越大,屋顶TMD荷载分布越均匀,减震效果越好;屋顶保温层TMD减震效果最好,双水箱屋顶TMD的减震效果次之,单水箱屋顶TMD的减震效果最差.本项研究成果可以为TMD的后续研究和设计提供理论依据.